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(-) Description

Title :  STRUCTURE BASED DESIGN OF SUB-NANOMOLAR AFFINITY ANTI-METHAMPHETAMINE SINGLE CHAIN ANTIBODIES.
 
Authors :  S. Thakkar, K. I. Varughese
Date :  23 Aug 12  (Deposition) - 02 Oct 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H
Keywords :  Antibody Meth Complex, Immunoglobulin Fold, Anti-Meth Single Chain Antibody, Free Meth Concentration, Methamphetamine, Vasculature, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Thakkar, N. Nanaware-Kharade, R. Celikel, E. C. Peterson, K. I. Varughese
Affinity Improvement Of A Therapeutic Antibody To Methamphetamine And Amphetamine Through Structure-Based Antibody Engineering.
Sci Rep V. 4 3673 2014
PubMed-ID: 24419156  |  Reference-DOI: 10.1038/SREP03673

(-) Compounds

Molecule 1 - ANTI-METH SCFV
    Chains: H
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZ ALPHA
    Expression System Strain: X33
    Expression System Taxid: 4919
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1B401Ligand/Ion(2S)-N-METHYL-1-PHENYLPROPAN-2-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:33 , SER H:35 , TYR H:47 , TYR H:50 , PHE H:95 , GLU H:101 , TYR H:1034 , TYR H:1036 , HIS H:1089 , TRP H:1091BINDING SITE FOR RESIDUE B40 H 1201

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:1023 -H:1088

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser H:1007 -Pro H:1008
2Phe H:1094 -Pro H:1095

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GQP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GQP)

(-) Exons   (0, 0)

(no "Exon" information available for 4GQP)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...ee.....eeeeeeeee......eeeeeee.....eeeeeeee....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......eee...eeeee........ee....eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
               4gqp H     1 EVQLQESGPSLVKPSQTLSLTCSVTGDSVTSGYWSWIRQFPGNKLDYMGYISYRGSTYYNPSLKSRISITRDTSKNQVYLQLKSVSSEDTATYYCTYFDSDDYAMEYWGQGTSVTVSGGGSQIVLTQSPAIMSASPGEKVTLTCSASSSVSSSHLYWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAASYFCHQWSSFPFTFGSGTKLEIK 1106A
                                    10        20        30        40        50        60        70        80  |||   87        97  |||  105     1001B|     1009      1019      1028      1038      1048      1058      1068      1078      1088      1098        |
                                                                                                            82A||              100A||         112||||                       1027A                                                                           1106A
                                                                                                             82B|               100B|        1001D|||                                                                                                            
                                                                                                              82C                100C         1001C||                                                                                                            
                                                                                                                                               1001B|                                                                                                            
                                                                                                                                                1001A
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4GQP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GQP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GQP)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  4gqp
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 Related Entries

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(-) Related Entries Specified in the PDB File

3gkz THE WILD TYPE OF ANTI-METH SCFV